View source for 9qgz


==Crystal structure of a D-lactate dehydrogenase from Porcellio dilatatus==
<StructureSection load='9qgz' size='340' side='right'caption='[[9qgz]], [[Resolution|resolution]] 2.84&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9qgz]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Porcellio_dilatatus Porcellio dilatatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9QGZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9QGZ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.84&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9qgz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9qgz OCA], [https://pdbe.org/9qgz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9qgz RCSB], [https://www.ebi.ac.uk/pdbsum/9qgz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9qgz ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod Porcellio dilatatus. The enzyme was identified through in silico screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome c or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor. IMPORTANCE: This study illustrates how metagenomics, structural biology, and computational tools can jointly drive the discovery of new enzymes with valuable biotechnological applications aligned with circular economic principles. The newly identified D-lactate dehydrogenase, PdG-D-LDH, exhibits thermostability, stereoselectivity, and high catalytic efficiency, providing new insights into the structure-function relationships of lactate-metabolizing enzymes.

Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.,Coelho C, Taborda A, Lorena C, Frazao T, Verissimo A, Borges PT, Brissos V, Tiago I, Martins LO Appl Environ Microbiol. 2025 Nov 13:e0148025. doi: 10.1128/aem.01480-25. PMID:41231970<ref>PMID:41231970</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
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== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Porcellio dilatatus]]
[[Category: Borges PT]]
[[Category: Frazao C]]
[[Category: Martins LO]]